Microbial community assembly and pathogen signatures in groundwater and tap water systems in greater Cairo, Egypt

Microbial communities in aquatic ecosystems are integral to water quality and public health, yet their structure and underlying ecological processes in regions like Egypt remain underexplored. To address this gap, this research explores the structure and dynamics of prokaryotic communities in tap water and groundwater in Cairo, Egypt.

Using environmental DNA metabarcoding, bioinformatics, and statistical modeling, we investigated microbial composition, pathogen identification, environmental factors, and ecological assembly processes.

The sequence analysis revealed the presence of 6,868 amplicon sequence variants (ASVs), with distinct community structures between groundwater and tap water. Proteobacteria dominated both habitats, with significant habitat-specific variations in Firmicutes, Actinobacteria, Verrucomicrobia, and Bacteroidota. Key genera included Methylobacterium in tap water, and Thauera and Legionella in groundwater, reflecting habitat-specific adaptations. The potential presence of Legionella-detected through 16 S rRNA gene signatures-may indicate conditions that could support organisms associated with diseases such as Legionnaires' disease; however, 16 S-based detection does not confirm viability or infectivity. Similarly, the surrogate presence of taxa such as Streptococcus salivarius, Stenotrophomonas maltophilia, and Acinetobacter baumannii in tap-water samples suggests possible post-treatment contamination or biofilm-associated persistence, warranting further targeted monitoring using methods capable of confirming viability. Ecological assessments indicated that stochastic mechanisms, particularly ecological drift, were the dominant forces shaping microbial community assembly in both water sources, whereas homogeneous selection exerted a moderate influence specifically within groundwater environments. Environmental parameters such as DO%, NO₂-N, and NO₃-N were critical in shaping tap water communities, while NH₄-N and TDS influenced groundwater communities.

This study highlights the distinct microbial dynamics of groundwater and tap water, emphasizing the importance of integrated water quality management strategies to mitigate nutrient pollution, monitor potential pathogen signatures, and protect public health.